Various Explanations

Great Talent and Godsend

When Hiro locates his katana in a New York Citymuseum, Ando believes that the Symbol is actually a combination of two Japanese characters — sai (才), which translates to great talent, and yo (与), which translates to godsend. (Godsend)

The Kanji dictionary defines yo as "bestow; participate in; give; award; impart; provide; cause; gift; godsend" and sai as "genius; years old" leading to a broader definition of the symbol under Ando's explanation, possibly as "bestowing talent/genius" or "providing/imparting ability".

The Serpent and the Crane

While sketching the symbol in the sand, Guillame tells his son the story of the serpent and the crane. The serpent was a creature of ambition, tired of crawling on its belly and eating grubs and mice. One day, he spotted the crane. The crane was carefree and stupid, but could fly. The sun shone on her always; she slept in the clouds and drank from the rainbows. The serpent found the crane at her watering hole, swallowed her whole, and was able to fly using her wings. The serpent flew around the sun and to the moon; he ate the clouds and played in the rain. However, Guillame notes, "What good is it to fly, if you have nowhere to go?" He says that the serpent lost touch with the ground. Guillame then scratches through his sketch. (It Takes a Village, Part 3)

In an interview concerning the Symbol, Tim Kring says, "I would just say that part of the fun of watching the show is seeing how certain things crop up. And if you look at that symbol carefully, you might be able to figure it out. By the way, the symbol also shows up in places viewers can't see: On the door of a room in the soundstage where Heroes shoots, the sign reads 'PROPS' — with that special S as the symbol."

It seems that the symbol of Pinehearst Company is two of these symbols overlapping to form a representation of DNA.

The eBook Brave New World describes the symbol as a "glyph" that "resembled a broken strand of DNA helix, but different from any found in most normal humans."

Trivia

When the shot zooms in on the symbol on the hilt of the replica sword in the Museum, the symbol is reversed. (Godsend) This may be due to the reverse side of the hilt being a mirror image of the other side.